For instance, watching Doctor Who -- the old, classic Doctor Who -- it's obvious how many of them keep the story conflict lively by having more than two factions in on the fray. The shipwrecked humans, the marsh creatures -- the youngsters among the humans who have convinced themselves that their elders were lying in order to control them. Or the undersea base where the aliens are invading, and the two saboteurs carry on. Sometimes with only a sprinkling of villains here and there, and most characters who are problems more pigheaded than evil. Though all too often, one side is only too willing to treat the faction they are most preoccupied with as the one that's most dangerous, in defiance of the facts.
And that's before the Doctor shows up. To be mistaken, frequently enough, for a spy or saboteur himself. But he's always on a side all of his own.
It definitely does the job in keeping the plot going. For all Doctor Who's ramshackle plots, several different people who all want different, conflicting things will always keep the conflict going.